51
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Wood K, Plazanet M, Gabel F, Kessler B, Oesterhelt D, Zaccai G, Weik M. Dynamics of hydration water in deuterated purple membranes explored by neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:619-26. [PMID: 18286273 PMCID: PMC2755797 DOI: 10.1007/s00249-008-0285-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 01/22/2008] [Accepted: 01/31/2008] [Indexed: 11/29/2022]
Abstract
The function and dynamics of proteins depend on their direct environment, and much evidence has pointed to a strong coupling between water and protein motions. Recently however, neutron scattering measurements on deuterated and natural-abundance purple membrane (PM), hydrated in H2O and D2O, respectively, revealed that membrane and water motions on the ns-ps time scale are not directly coupled below 260 K (Wood et al. in Proc Natl Acad Sci USA 104:18049-18054, 2007). In the initial study, samples with a high level of hydration were measured. Here, we have measured the dynamics of PM and water separately, at a low-hydration level corresponding to the first layer of hydration water only. As in the case of the higher hydration samples previously studied, the dynamics of PM and water display different temperature dependencies, with a transition in the hydration water at 200 K not triggering a transition in the membrane at the same temperature. Furthermore, neutron diffraction experiments were carried out to monitor the lamellar spacing of a flash-cooled deuterated PM stack hydrated in H2O as a function of temperature. At 200 K, a sudden decrease in lamellar spacing indicated the onset of long-range translational water diffusion in the second hydration layer as has already been observed on flash-cooled natural-abundance PM stacks hydrated in D2O (Weik et al. in J Mol Biol 275:632-634, 2005), excluding thus a notable isotope effect. Our results reinforce the notion that membrane-protein dynamics may be less strongly coupled to hydration water motions than the dynamics of soluble proteins.
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Affiliation(s)
- K Wood
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France
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52
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Doster W. The dynamical transition of proteins, concepts and misconceptions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:591-602. [PMID: 18270694 DOI: 10.1007/s00249-008-0274-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2007] [Revised: 01/10/2008] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
Abstract
The dynamics of hydrated proteins and of protein crystals can be studied within a wide temperature range, since the water of hydration does not crystallize at low temperature. Instead it turns into an amorphous glassy state below 200 K. Extending the temperature range facilitates the spectral separation of different molecular processes. The conformational motions of proteins show an abrupt enhancement near 180 K, which has been called a "dynamical transition". In this contribution various aspects of the transition are critically reviewed: the role of the instrumental resolution function in extracting displacements from neutron elastic scattering data and the question of the appropriate dynamic model, discrete transitions between states of different energy versus continuous diffusion inside a harmonic well, are discussed. A decomposition of the transition involving two motional components is performed: rotational transitions of methyl groups and small scale librations of side-chains, induced by water at the protein surface. Both processes create an enhancement of the observed amplitude. The onset occurs, when their time scale becomes compatible with the resolution of the spectrometer. The reorientational rate of hydration water follows a super-Arrhenius temperature dependence, a characteristic feature of a dynamical transition. It occurs only with hydrated proteins, while the torsional motion of methyl groups takes place also in the dehydrated or solvent-vitrified system. Finally, the role of fast hydrogen bond fluctuations contributing to the amplitude enhancement is discussed.
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Affiliation(s)
- Wolfgang Doster
- Physics Department E13, Technical University Munich, 85748 Garching, Germany.
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53
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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54
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Coupling of protein and hydration-water dynamics in biological membranes. Proc Natl Acad Sci U S A 2007; 104:18049-54. [PMID: 17986611 DOI: 10.1073/pnas.0706566104] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H(2)O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D(2)O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps-ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at approximately 200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water.
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55
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Abstract
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.
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Affiliation(s)
- Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
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56
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Oleinikova A, Smolin N, Brovchenko I. Origin of the dynamic transition upon pressurization of crystalline proteins. J Phys Chem B 2007; 110:19619-24. [PMID: 17004829 DOI: 10.1021/jp0629590] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We study the role of hydration water in the dynamic transition of low-hydrated proteins upon pressurization found recently (Meinhold, L.; Smith, J. C. Phys. Rev. E 2005, 72, 061908). Clustering and percolation of water in the hydration shells of protein molecules in crystalline Staphylococcal nuclease are analyzed at various pressures. The number of water molecules in the hydration shell increases and the hydrogen-bonded network of hydration water spans with increasing pressure. The dynamic transition of protein occurs when the spanning water network exists with the probability of about 50% and hydration water shows large density fluctuations. Formation of a spanning water network upon pressurization promotes protein dynamics as in the case of the dynamic transition with increasing hydration. Properties of hydration water in various thermodynamic states and their influence on biological function are discussed.
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Affiliation(s)
- Alla Oleinikova
- Department of Physical Chemistry, University of Dortmund, Otto-Hahn-Strasse 6, Dortmund D-44227, Germany.
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57
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Magazù S, Romeo G, Telling MTF. Temperature dependence of protein dynamics as affected by sugars: a neutron scattering study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:685-91. [PMID: 17657485 DOI: 10.1007/s00249-007-0190-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 04/29/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
Neutron scattering data on lysozyme-trehalose and lysozyme-sucrose aqueous mixtures, and on trehalose and sucrose aqueous mixtures are presented for a wide temperature range. Although the degree of protein coupling to solvent seems to be an open question in the literature, we present evidence that seems to be a firm link between a local dynamics of the protein with that of the glassy host. One of the objectives of this study was to explore the relationship between protein dynamics and glassy host. Measuring the <u(2)> of lysozyme mixtures, we arrive at a qualitative description of how their thermal stability is affected by the presence of two sugars at different temperatures. Whereas the Q dependence of the elastic incoherent structure factor gives information about the geometry and the amplitudes of the motions.
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Affiliation(s)
- S Magazù
- Physics Department and INFM, Messina University, Messina, Italy
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58
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Mauring K, Deich J, Rosell FI, McAnaney TB, Moerner WE, Boxer SG. Enhancement of the fluorescence of the blue fluorescent proteins by high pressure or low temperature. J Phys Chem B 2007; 109:12976-81. [PMID: 16852610 DOI: 10.1021/jp0448595] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Green fluorescent proteins bearing the Y66H mutation exhibit strongly blue-shifted fluorescence excitation and emission spectra. However, these blue fluorescent proteins (BFPs) have lower quantum yields of fluorescence (Phi(f) approximately 0.20), which is believed to stem from the increased conformational freedom of the smaller chromophore. We demonstrate that suppression of chromophore mobility by increasing hydrostatic pressure or by decreasing temperature can enhance the fluorescence quantum yield of these proteins without significantly affecting their absorption properties or the shape of the fluorescence spectra. Analysis of the fluorescence lifetimes in the picosecond and nanosecond regimes reveals that the enhancement of the fluorescence quantum yield is due to the inhibition of fast quenching processes. Temperature-dependent fluorescence measurements reveal two barriers ( approximately 19 and 3 kJ/mol, respectively) for the transition into nonfluorescing states. These steps are probably linked with dissociation of the hydrogen bond between the chromophore and His148 or an intervening water molecule and to the barrier for chromophore twisting in the excited state, respectively. The chromophore's hydrogen-bond equilibrium at room temperature is dominated by entropic effects, while below approximately 200 K the balance is enthalpy-driven.
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Affiliation(s)
- Koit Mauring
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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59
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Senesi R, Pietropaolo A, Bocedi A, Pagnotta SE, Bruni F. Proton momentum distribution in a protein hydration shell. PHYSICAL REVIEW LETTERS 2007; 98:138102. [PMID: 17501242 DOI: 10.1103/physrevlett.98.138102] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Indexed: 05/15/2023]
Abstract
The momentum distribution of protons in the hydration shell of a globular protein has been measured through deep inelastic neutron scattering at 180 and 290 K, below and above the crossover temperature Tc=1.23Tg, where Tg=219 K is the glass transition temperature. It is found that the mean kinetic energy of the water hydrogens shows no temperature dependence, but the measurements are accurate enough to indicate a sensible change of momentum distribution and effective potential felt by protons, compatible with the transition from a single to a double potential well. This could support the presence of tunneling effects even at room temperature, playing an important role in biological function.
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Affiliation(s)
- R Senesi
- Dipartimento di Fisica and Centro NAST, Università degli Studi di Roma Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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60
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Kumar P, Yan Z, Xu L, Mazza MG, Buldyrev SV, Chen SH, Sastry S, Stanley HE. Glass transition in biomolecules and the liquid-liquid critical point of water. PHYSICAL REVIEW LETTERS 2006; 97:177802. [PMID: 17155508 DOI: 10.1103/physrevlett.97.177802] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Indexed: 05/10/2023]
Abstract
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the macromolecules, sometimes called a "protein glass transition," occurs at the temperature of dynamic crossover in the diffusivity of hydration water and also coincides with the maxima of the isobaric specific heat C_{P} and the temperature derivative of the orientational order parameter. We relate these findings to the hypothesis of a liquid-liquid critical point in water. Our simulations are consistent with the possibility that the protein glass transition results from crossing the Widom line, which is defined as the locus of correlation length maxima emanating from the hypothesized second critical point of water.
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Affiliation(s)
- Pradeep Kumar
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
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61
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Roh JH, Curtis JE, Azzam S, Novikov VN, Peral I, Chowdhuri Z, Gregory RB, Sokolov AP. Influence of hydration on the dynamics of lysozyme. Biophys J 2006; 91:2573-88. [PMID: 16844746 PMCID: PMC1562387 DOI: 10.1529/biophysj.106.082214] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quasielastic neutron and light-scattering techniques along with molecular dynamics simulations were employed to study the influence of hydration on the internal dynamics of lysozyme. We identified three major relaxation processes that contribute to the observed dynamics in the picosecond to nanosecond time range: 1), fluctuations of methyl groups; 2), fast picosecond relaxation; and 3), a slow relaxation process. A low-temperature onset of anharmonicity at T approximately 100 K is ascribed to methyl-group dynamics that is not sensitive to hydration level. The increase of hydration level seems to first increase the fast relaxation process and then activate the slow relaxation process at h approximately 0.2. The quasielastic scattering intensity associated with the slow process increases sharply with an increase of hydration to above h approximately 0.2. Activation of the slow process is responsible for the dynamical transition at T approximately 200 K. The dependence of the slow process on hydration correlates with the hydration dependence of the enzymatic activity of lysozyme, whereas the dependence of the fast process seems to correlate with the hydration dependence of hydrogen exchange of lysozyme.
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Affiliation(s)
- J H Roh
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, USA
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62
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Cornicchi E, Marconi M, Onori G, Paciaroni A. Controlling the protein dynamical transition with sugar-based bioprotectant matrices: a neutron scattering study. Biophys J 2006; 91:289-97. [PMID: 16617083 PMCID: PMC1479059 DOI: 10.1529/biophysj.106.081752] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 03/20/2006] [Indexed: 11/18/2022] Open
Abstract
Through elastic neutron scattering we measured the mean-square displacements of the hydrogen atoms of lysozyme embedded in a glucose-water glassy matrix as a function of the temperature and at various water contents. The elastic intensity of all the samples has been interpreted in terms of the double-well model in the whole temperature range. The dry sample shows an onset of anharmonicity at approximately 100 K, which can be attributed to the activation of methyl group reorientations. Such a protein intrinsic dynamics is decoupled from the external environment on the whole investigated temperature range. In the hydrated samples an additional and larger anharmonic contribution is provided by the protein dynamical transition, which appears at a higher temperature Td. As hydration increases the coupling between the protein internal dynamics and the surrounding matrix relaxations becomes more effective. The behavior of Td that, as a function of the water content, diminishes by approximately 60 K, supports the picture of the protein dynamics as driven by solvent relaxations. A possible connection between the protein dynamical response versus T and the thermal stability in glucose-water bioprotectant matrices is proposed.
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Affiliation(s)
- E Cornicchi
- Dipartimento di Fisica dell'Università di Perugia, CEMIN (Centro di Eccellenza per i Materiali Innovativi Nanostrutturati) and INFM CRS-SOFT, 06123 Perugia, Italy
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63
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Paciaroni A, Cornicchi E, De Francesco A, Marconi M, Onori G. Conditioning action of the environment on the protein dynamics studied through elastic neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:591-9. [PMID: 16761157 DOI: 10.1007/s00249-006-0073-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/19/2006] [Accepted: 05/04/2006] [Indexed: 11/25/2022]
Abstract
The dynamics of lysozyme in the picosecond timescale has been studied when it is in dry and hydrated powder form and when it is embedded in glycerol, glycerol-water, glucose and glucose-water matrices. The investigation has been undertaken through elastic neutron scattering technique on the backscattering spectrometer IN13. The dynamics of dry powder and embedded-in-glucose lysozyme can be considered purely vibrational up to 100 K, where the onset of an anharmonic contribution takes place. This contribution can be attributed to the activation of methyl group reorientations and is described with an Arrhenius trend. An additional source of anharmonic dynamics appears at higher temperatures for lysozyme in hydrated powders and embedded in glycerol, glycerol-water and glucose-water matrices. This second process, also represented with an Arrhenius trend, corresponds to the so-called protein dynamical transition. Both the temperature where such a transition takes place and the magnitude of the protein mean square displacements depend on the environment. The dynamical response of the protein to temperature is put in relationship with its thermal stability.
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Affiliation(s)
- A Paciaroni
- Dipartimento di Fisica dell'Università di Perugia, CNR-INFM CRS SOFT, Via A. Pascoli, 06123, Perugia, Italy.
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64
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van der Spoel D, van Maaren PJ, Larsson P, Tîmneanu N. Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media. J Phys Chem B 2006; 110:4393-8. [PMID: 16509740 DOI: 10.1021/jp0572535] [Citation(s) in RCA: 311] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thermodynamics of hydrogen bond breaking and formation was studied in solutions of alcohol (methanol, ethanol, 1-propanol) molecules. An extensive series of over 400 molecular dynamics simulations with an aggregate length of over 900 ns was analyzed using an analysis technique in which hydrogen bond (HB) breaking is interpreted as an Eyring process, for which the Gibbs energy of activation DeltaG can be determined from the HB lifetime. By performing simulations at different temperatures, we were able to determine the enthalpy of activation DeltaH and the entropy of activation TDeltaS for this process from the Van't Hoff relation. The equilibrium thermodynamics was determined separately, based on the number of donor hydrogens that are involved in hydrogen bonds. Results (DeltaH) are compared to experimental data from Raman spectroscopy and found to be in good agreement for pure water and methanol. The DeltaG as well as the DeltaG are smooth functions of the composition of the mixtures. The main result of the calculations is that DeltaG is essentially independent of the environment (around 5 kJ/mol), suggesting that buried hydrogen bonds (e.g., in proteins) do not contribute significantly to protein stability. Enthalpically HB formation is a downhill process in all substances; however, for the alcohols there is an entropic barrier of 6-7 kJ/mol, at 298.15 K, which cannot be detected in pure water.
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Affiliation(s)
- David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-751 24 Uppsala, Sweden.
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65
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Magazù S, Migliardo F, Telling MTF. α,α-Trehalose−Water Solutions. VIII. Study of the Diffusive Dynamics of Water by High-Resolution Quasi Elastic Neutron Scattering. J Phys Chem B 2005; 110:1020-5. [PMID: 16471637 DOI: 10.1021/jp0536450] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present paper shows high-resolution quasi-elastic neutron scattering (QENS) findings on homologues disaccharides (i.e. trehalose, maltose, and sucrose)-water mixtures as a function of temperature. The QENS measurements were performed on both partially deuterated disaccharides in D2O and on hydrogenated disaccharides in H2O to separate the solute dynamics from that of the solvent. The results highlight a noticeable disaccharide kosmotrope character, with results more marked for trehalose. Such evidence accounts for its higher bioprotective effectiveness.
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Affiliation(s)
- Salvatore Magazù
- Dipartimento di Fisica, Università di Messina, P.O. Box 55, I-98166 Messina, Italy. smagazu@.unime.it
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66
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Low frequency enzyme dynamics as a function of temperature and hydration: A neutron scattering study. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.05.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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67
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Chen P, Zhang L, Cao F. Effects of Moisture on Glass Transition and Microstructure of Glycerol-Plasticized Soy Protein. Macromol Biosci 2005; 5:872-80. [PMID: 16143997 DOI: 10.1002/mabi.200500072] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The glass transition behavior of the glycerol-plasticized soy protein sheets (SL series) at various relative humidity (RH) was investigated by using differential scanning calorimetry with the aluminum pan and O-ring-sealed stainless steel capsule, and the microstructure of these sheets was detected on small-angle X-ray scattering. The results revealed that there were three glass transitions (Tg1, Tg2 and Tg3), corresponding to glycerol-rich, protein-rich and protein-water domains, in the protein-glycerol-water ternary system. The Tg1 values of the SL-series sheets at 75% RH decreased from -49.3 to -83.8 degrees C with an increase of glycerol content from 10 to 50 wt.-%, whereas Tg2 and Tg3 were almost invariable at about 60 degrees C and 3 degrees C, respectively. In addition, the Tg1, Tg2 and Tg3 values of the SL-25 containing 25 wt.-% glycerol at 0%, 35%, 58%, 75% and 98% RH were in the range of -12.7 - -83.2 degrees C, 65.8 - 53.1 degrees C and 3.5 - 1.9 degrees C, respectively. The result from small-angle X-ray scattering indicated that the radii of gyration (Rg) of protein-rich domain were in the range of 60-63 nm; this suggested the existence of protein macromolecules as aggregates in the stable protein-rich and protein-water domains. With an increase of RH, the tensile strength and Tg values of the SL-series sheets decreased, but the elongation at break increased. In view of the results above, the moisture in ambient environment significantly influenced the Tg values and microstructures of the glycerol-plasticized soy protein sheets, leading to the changes of the mechanical and thermal properties.
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Affiliation(s)
- Pu Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
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68
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Abstract
Various types of large-amplitude molecular deformation are ubiquitously involved in the functions of biological macromolecules, especially supramolecular complexes. They can be very effectively analyzed by normal mode analysis with well-established procedures. However, despite its enormous success in numerous applications, certain issues related to the applications of normal mode analysis require further discussion. In this review, the author addresses some common issues so as to raise the awareness of the usefulness and limitations of the method in the general community of structural biology.
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Affiliation(s)
- Jianpeng Ma
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.
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69
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Koutsopoulos S, van der Oost J, Norde W. Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering. Proteins 2005; 61:377-84. [PMID: 16106445 DOI: 10.1002/prot.20606] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The dynamic behavior of an endoglucanase from the hyperthermophilic microorganism Pyrococcus furiosus was investigated using elastic neutron scattering. The temperature dependence of the atomic motions was correlated with conformational and functional characteristics of the enzyme. The onset of biological function at temperatures higher than approximately 25 degrees C (the hyperthermostable enzyme is essentially inactive at room temperature) was associated with a dynamical transition in the anharmonic motions domain. This transition from the nonactive to the enzymatically active conformation involved structurally similar conformational substates in the energy landscape. From the mean-square displacement of the protein atoms, the molecular flexibility and the effective force constants were calculated at different temperature zones. The results showed that the activity increases at higher temperatures where the intramolecular bonds are weakened and the overall rigidity of the protein is decreased. Further temperature increase resulted in significantly increased atomic fluctuations featuring heat denaturation of the protein.
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Affiliation(s)
- Sotirios Koutsopoulos
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Wageningen, The Netherlands.
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70
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Hill JJ, Shalaev EY, Zografi G. Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration. J Pharm Sci 2005; 94:1636-67. [PMID: 15965985 DOI: 10.1002/jps.20333] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.
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Affiliation(s)
- John J Hill
- ICOS Corporation, 22021 20th Avenue SE, Bothell, WA 98021, USA.
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71
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Weik M, Lehnert U, Zaccai G. Liquid-like water confined in stacks of biological membranes at 200 k and its relation to protein dynamics. Biophys J 2005; 89:3639-46. [PMID: 16055529 PMCID: PMC1366856 DOI: 10.1529/biophysj.104.055749] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Confined water is of considerable current interest owing to its biophysical importance and relevance to cryopreservation. It can be studied in its amorphous or supercooled state in the "no-man's land", i.e., in the temperature range between 150 and 235 K, in which bulk water is always crystalline. Amorphous deuterium oxide (D(2)O) was obtained in the intermembrane spaces of a stack of purple membranes from Halobacterium salinarum by flash cooling to 77 K. Neutron diffraction showed that upon heating to 200 K the intermembrane water space decreased sharply with an associated strengthening of ice diffraction, indicating that water beyond the first membrane hydration layer flowed out of the intermembrane space to form crystalline ice. It was concluded that the confined water undergoes a glass transition at or below 200 K to adopt an ultraviscous liquid state from which it crystallizes to form ice as soon as it finds itself in an unconfined, bulk-water environment. Our results provide model-free evidence for translational diffusion of confined water in the no-man's land. Potential effects of the confined-water glass transition on nanosecond membrane dynamics were investigated by incoherent elastic neutron scattering experiments. These revealed no differences between flash-cooled and slow-cooled samples (in the latter, the intermembrane space at temperatures <250 K is occupied only by the first membrane hydration layers), with dynamical transitions at 150 and 260 K, but not at 200 K, suggesting that nanosecond membrane dynamics are not sensitive to the state of the water beyond the first hydration shell at cryotemperatures.
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Affiliation(s)
- M Weik
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale CEA-CNRS-UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.
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72
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Berntsen P, Bergman R, Jansson H, Weik M, Swenson J. Dielectric and calorimetric studies of hydrated purple membrane. Biophys J 2005; 89:3120-8. [PMID: 16055533 PMCID: PMC1366809 DOI: 10.1529/biophysj.104.057208] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Purple membranes (PM) from halobacteria were hydrated to approximately 0.4 and approximately 0.2 g H(2)O/g of PM and studied by dielectric spectroscopy and differential scanning calorimetry between 120 and 300 K. The dielectric process, attributed to a local (beta) relaxation of the confined supercooled water, shows an Arrhenius temperature behavior at low temperatures. In the case of the most hydrated PM a small deviation from the Arrhenius behavior occurs at 190-200 K together with a pronounced endothermic process and an increased activation energy. The observed crossover is accompanied by a reduction of the interlayer spacing due to the partial loss of the intermembrane water. All these effects at approximately 200 K are consistent with a scenario where the local relaxation process merges with a nonobservable alpha-relaxation of the interlayer water, giving rise to a more liquid-like behavior of the interfacial water. For the less hydrated sample the effects are less pronounced and shift to a slightly higher temperature.
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Affiliation(s)
- Peter Berntsen
- Department of Applied Physics, Chalmers University of Technology and Göteborg University, SE-51296 Göteborg, Sweden.
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73
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Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme activity and flexibility at very low hydration. Biophys J 2005; 89:1282-7. [PMID: 15894640 PMCID: PMC1366612 DOI: 10.1529/biophysj.104.058677] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.
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Affiliation(s)
- V Kurkal
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Germany
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74
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Chen P, Zhang L. New Evidences of Glass Transitions and Microstructures of Soy Protein Plasticized with Glycerol. Macromol Biosci 2005; 5:237-45. [PMID: 15768443 DOI: 10.1002/mabi.200400179] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Soy protein isolate (SPI) and glycerol were mixed under mild (L series) and severe (H series) mixing conditions, respectively, and then were compression-molded at 140 degrees C and 20 MPa to prepare the sheets (SL and SH series). The glass transition behaviors and microstructures of the soy protein plasticized with glycerol were investigated carefully by using differential scanning calorimetry and small-angle X-ray scattering. The results revealed that there were two glass transitions in the SPI/glycerol systems. When the glycerol contents ranged from 25 to 40 wt.-%, all of the SL- and SH-series sheets showed two glass transition temperatures (T(g1) and T(g2)) corresponding to glycerol-rich and protein-rich domains, respectively. The T(g1) values of the sheets decreased from -28.5 to -65.2 degrees C with an increase of glycerol content from 25 to 50 wt.-%, whereas the T(g2) values were almost invariable at about 44 degrees C. The results from wide-angle X-ray diffraction and small-angle X-ray scattering indicated that both protein-rich and glycerol-rich domains existed as amorphous morphologies, and the radii of gyration (R(g)) of the protein-rich domains were around 60 nm, a result suggesting the existence of stable protein domains. The results above suggest that protein-rich domains were composed of the compact chains of protein with relatively low compatibility to glycerol and glycerol-rich domains consisted of relative loose chains that possessed good compatibility with glycerol. The significant microphase separation occurred in the SPI sheets containing more than 25 wt.-% glycerol, with a rapid decrease of the tensile strength and Young's modulus. [illustration in text].
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Affiliation(s)
- Pu Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
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75
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Cicerone MT, Soles CL. Fast dynamics and stabilization of proteins: binary glasses of trehalose and glycerol. Biophys J 2005; 86:3836-45. [PMID: 15189880 PMCID: PMC1304285 DOI: 10.1529/biophysj.103.035519] [Citation(s) in RCA: 216] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present elastic and inelastic incoherent neutron scattering data from a series of trehalose glasses diluted with glycerol. A strong correlation with recently published protein stability data in the same series of glasses illustrates that the dynamics at Q >or= 0.71 A(-1) and omega > 200 MHz are important to stabilization of horseradish peroxidase and yeast alcohol dehydrogenase in these glasses. To the best of our knowledge, this is the first direct evidence that enzyme stability in a room temperature glass depends upon suppressing these short-length scale, high-frequency dynamics within the glass. We briefly discuss the coupling of protein motions to the local dynamics of the glass. Also, we show that T(g) alone is not a good indicator for the protein stability in this series of glasses; the glass that confers the maximum room-temperature stability does not have the highest T(g).
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Affiliation(s)
- Marcus T Cicerone
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8543, USA.
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76
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Tournier AL, Réat V, Dunn R, Daniel R, Smith JC, Finney J. Temperature and timescale dependence of protein dynamics in methanol : water mixtures. Phys Chem Chem Phys 2005; 7:1388-93. [DOI: 10.1039/b416103c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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77
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Gabel F, Weik M, Doctor BP, Saxena A, Fournier D, Brochier L, Renault F, Masson P, Silman I, Zaccai G. The influence of solvent composition on global dynamics of human butyrylcholinesterase powders: a neutron-scattering study. Biophys J 2004; 86:3152-65. [PMID: 15111428 PMCID: PMC1304180 DOI: 10.1016/s0006-3495(04)74363-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A major result of incoherent elastic neutron-scattering experiments on protein powders is the strong dependence of the intramolecular dynamics on the sample environment. We performed a series of incoherent elastic neutron-scattering experiments on lyophilized human butyrylcholinesterase (HuBChE) powders under different conditions (solvent composition and hydration degree) in the temperature range from 20 to 285 K to elucidate the effect of the environment on the enzyme atomic mean-square displacements. Comparing D(2)O- with H(2)O-hydrated samples, we were able to investigate protein as well as hydration water molecular dynamics. HuBChE lyophilized from three distinct buffers showed completely different atomic mean-square displacements at temperatures above approximately 200 K: a salt-free sample and a sample containing Tris-HCl showed identical small-amplitude motions. A third sample, containing sodium phosphate, displayed highly reduced mean-square displacements at ambient temperature with respect to the other two samples. Below 200 K, all samples displayed similar mean-square displacements. We draw the conclusion that the reduction of intramolecular protein mean-square displacements on an Angstrom-nanosecond scale by the solvent depends not only on the presence of salt ions but also on their type.
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Affiliation(s)
- F Gabel
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale, Grenoble, France
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78
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Magazù S, Maisano G, Migliardo F, Mondelli C. Mean-square displacement relationship in bioprotectant systems by elastic neutron scattering. Biophys J 2004; 86:3241-9. [PMID: 15111437 PMCID: PMC1304189 DOI: 10.1016/s0006-3495(04)74372-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Neutron intensity elastic scans on trehalose, maltose, and sucrose/H(2)O mixtures as a function of concentration, temperature, and exchanged wave vector are presented. The experimental findings show a crossover in molecular fluctuations between harmonic and anharmonic dynamical regimes. A new operative definition for the degree of fragility of glass-forming systems is furnished by using explicitly the connection between viscosity and mean-square displacement. The procedure is tested for the investigated mixtures and for a set of glass-forming systems. In this frame, the stronger character of trehalose/H(2)O mixture indicates a better attitude in respect to maltose and sucrose/H(2)O mixtures to encapsulate biostructures in a more rigid matrix.
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Affiliation(s)
- S Magazù
- Dipartimento di Fisica and INFM, Università di Messina, Messina, Italy.
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79
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Weik M, Vernede X, Royant A, Bourgeois D. Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals. Biophys J 2004; 86:3176-85. [PMID: 15111430 PMCID: PMC1304182 DOI: 10.1016/s0006-3495(04)74365-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motions through the energy landscape of proteins lead to biological function. At temperatures below a dynamical transition (150-250 K), some of these motions are arrested and the activity of some proteins ceases. Here, we introduce the technique of temperature-derivative fluorescence microspectrophotometry to investigate the dynamical behavior of single protein crystals. The observation of glass transitions in thin films of water/glycerol mixtures allowed us to demonstrate the potential of the technique. Then, protein crystals were investigated, after soaking the samples in a small amount of fluorescein. If the fluorophore resides within the crystal channels, temperature-dependent changes in solvent dynamics can be monitored. Alternatively, if the fluorophore binds to the protein, local dynamical transitions within the biomolecule can be probed directly. A clear dynamical transition was observed at 175 K in the active site of crystalline human butyrylcholinesterase. The results suggest that the dynamics of crystalline proteins is strongly dependent on solvent composition and confinement in the crystal channels. Beyond applications in the field of kinetic crystallography, the highly sensitive temperature-derivative fluorescence microspectrophotometry technique opens the way to many studies on the dynamics of biological nanosamples.
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Affiliation(s)
- Martin Weik
- Laboratoire de Biophysique Moléculaire and Laboratoire de Cristallographie et Cristallogenèse des Protéines, UMR 5075, Institut de Biologie Structurale, 38027 Grenoble, France
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80
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Zaccai G. The effect of water on protein dynamics. Philos Trans R Soc Lond B Biol Sci 2004; 359:1269-75; discussion 1275, 1323-8. [PMID: 15306381 PMCID: PMC1693409 DOI: 10.1098/rstb.2004.1503] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neutron diffraction and spectroscopy were applied to describe the hydration and dynamics of a soluble protein and a natural membrane from extreme halophilic Archaea. The quantitative dependence of protein motions on water activity was clearly illustrated, and it was established that a minimum hydration shell is required for the systems to access their functional resilience, i.e. a dynamics state that allows biological activity.
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Affiliation(s)
- G Zaccai
- Institut de Biologie Structurale, 41 rue Jules Horowitz, Grenoble Cedex 1, France.
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81
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Smith JC, Merzel F, Bondar AN, Tournier A, Fischer S. Structure, dynamics and reactions of protein hydration water. Philos Trans R Soc Lond B Biol Sci 2004; 359:1181-9; discussion 1189-90. [PMID: 15306375 PMCID: PMC1693407 DOI: 10.1098/rstb.2004.1497] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The apparent simplicity of the water molecule belies the wide range of fascinating protein phenomena in which it participates. We review recent computer simulation work on buried, internal water molecules, discussing the thermodynamics of water molecule binding and the participation of water in proton transfer reactions. Surface water molecules are also considered, with emphasis on the modification of average solvent structure on a protein surface, the role of water in the protein dynamical 'glass' transition and a simplified description of the protein motions thereby activated.
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Affiliation(s)
- Jeremy C Smith
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, Universität Heidelberg, 69120 Heidelberg, Germany.
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82
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Becker T, Hayward JA, Finney JL, Daniel RM, Smith JC. Neutron frequency windows and the protein dynamical transition. Biophys J 2004; 87:1436-44. [PMID: 15345526 PMCID: PMC1304552 DOI: 10.1529/biophysj.104.042226] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 05/14/2004] [Indexed: 11/18/2022] Open
Abstract
Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, , that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations---an "equilibrium" model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a "frequency window" model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.
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Affiliation(s)
- Torsten Becker
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing, Universität Heidelberg, D-69120 Heidelberg, Germany
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83
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Navati MS, Ray A, Shamir J, Friedman JM. Probing Solvation-Shell Hydrogen Binding in Glassy and Sol−Gel Matrixes through Vibronic Sideband Luminescence Spectroscopy. J Phys Chem B 2003. [DOI: 10.1021/jp0366466] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahantesh S. Navati
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and Department of Chemistry, Hebrew University, Jerusalem, Israel
| | - Anandhi Ray
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and Department of Chemistry, Hebrew University, Jerusalem, Israel
| | - Jacob Shamir
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and Department of Chemistry, Hebrew University, Jerusalem, Israel
| | - Joel M. Friedman
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and Department of Chemistry, Hebrew University, Jerusalem, Israel
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84
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Tournier AL, Smith JC. Principal components of the protein dynamical transition. PHYSICAL REVIEW LETTERS 2003; 91:208106. [PMID: 14683404 DOI: 10.1103/physrevlett.91.208106] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2003] [Indexed: 05/12/2023]
Abstract
Proteins exhibit a solvent-driven dynamical transition at 180-220 K, manifested by nonlinearity in the temperature dependence of the average mean-square displacement. Here, molecular dynamics simulations of hydrated myoglobin show that the onset of the transition at approximately 180 K is characterized by the appearance of a single double-well principal component mode involving a global motion of two groups of helices. As the temperature is raised a few more quasiharmonic and multiminimum components successively appear. The results indicate an underlying simplicity in the protein dynamical transition.
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Affiliation(s)
- Alexander L Tournier
- Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), Im Neuenheimer Feld 368, Universität Heidelberg, 69120 Heidelberg, Germany
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85
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Daniel RM, Dunn RV, Finney JL, Smith JC. The role of dynamics in enzyme activity. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:69-92. [PMID: 12471064 DOI: 10.1146/annurev.biophys.32.110601.142445] [Citation(s) in RCA: 264] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.
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Affiliation(s)
- R M Daniel
- Department of Biological Sciences, University of Waikato, Hamilton 2001, New Zealand.
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86
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Giuffrida S, Cottone G, Librizzi F, Cordone L. Coupling between the Thermal Evolution of the Heme Pocket and the External Matrix Structure inTrehalose CoatedCarboxymyoglobin. J Phys Chem B 2003. [DOI: 10.1021/jp036194x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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87
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Yu X, Park J, Leitner DM. Thermodynamics of Protein Hydration Computed by Molecular Dynamics and Normal Modes. J Phys Chem B 2003. [DOI: 10.1021/jp035471x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin Yu
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557
| | - Jongsoon Park
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557
| | - David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557
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88
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Alkema WBL, de Vries E, Floris R, Janssen DB. Kinetics of enzyme acylation and deacylation in the penicillin acylase-catalyzed synthesis of beta-lactam antibiotics. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:3675-83. [PMID: 12950251 DOI: 10.1046/j.1432-1033.2003.03728.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Penicillin acylase catalyses the hydrolysis and synthesis of semisynthetic beta-lactam antibiotics via formation of a covalent acyl-enzyme intermediate. The kinetic and mechanistic aspects of these reactions were studied. Stopped-flow experiments with the penicillin and ampicillin analogues 2-nitro-5-phenylacetoxy-benzoic acid (NIPAOB) and d-2-nitro-5-[(phenylglycyl)amino]-benzoic acid (NIPGB) showed that the rate-limiting step in the conversion of penicillin G and ampicillin is the formation of the acyl-enzyme. The phenylacetyl- and phenylglycyl-enzymes are hydrolysed with rate constants of at least 1000 s-1 and 75 s-1, respectively. A normal solvent deuterium kinetic isotope effect (KIE) of 2 on the hydrolysis of 2-nitro-5-[(phenylacetyl)amino]-benzoic acid (NIPAB), NIPGB and NIPAOB indicated that the formation of the acyl-enzyme proceeds via a general acid-base mechanism. In agreement with such a mechanism, the proton inventory of the kcat for NIPAB showed that one proton, with a fractionation factor of 0.5, is transferred in the transition state of the rate-limiting step. The overall KIE of 2 for the kcat of NIPAOB resulted from an inverse isotope effect at low concentrations of D2O, which is overridden by a large normal isotope effect at large molar fractions of D2O. Rate measurements in the presence of glycerol indicated that the inverse isotope effect originated from the higher viscosity of D2O compared to H2O. Deacylation of the acyl-enzyme was studied by nucleophile competition and inhibition experiments. The beta-lactam compound 7-aminodesacetoxycephalosporanic acid (7-ADCA) was a better nucleophile than 6-aminopenicillanic acid, caused by a higher affinity of the enzyme for 7-ADCA and complete suppression of hydrolysis of the acyl-enzyme upon binding of 7-ADCA. By combining the results of the steady-state, presteady state and nucleophile binding experiments, values for the relevant kinetic constants for the synthesis and hydrolysis of beta-lactam antibiotics were obtained.
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Affiliation(s)
- Wynand B L Alkema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
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89
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Weik M. Low-temperature behavior of water confined by biological macromolecules and its relation to protein dynamics. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2003; 12:153-8. [PMID: 15007694 DOI: 10.1140/epje/i2003-10043-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Confined water is an essential component of biological entities and processes and its properties differ from the ones of bulk water. Since protein and water dynamics are thought to be strongly coupled, and since macromolecular dynamics is crucial for biological function, the study of water confined by biological macromolecules is not only interesting on its own right but often provides useful information for understanding biological activity at the molecular level. Studies are reviewed that focus on the low-temperature behavior of water confined in protein crystals and in stacks of native biological membranes. Diffraction methods allowed the determination of characteristic changes that relate to the glass transition and crystallization of water. Protein crystallography and energy-resolved neutron scattering are employed to gain further insight into the coupling of solvent and protein dynamics.
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Affiliation(s)
- M Weik
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027, Grenoble Cedex 1, France.
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90
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Tournier AL, Xu J, Smith JC. Translational hydration water dynamics drives the protein glass transition. Biophys J 2003; 85:1871-5. [PMID: 12944299 PMCID: PMC1303358 DOI: 10.1016/s0006-3495(03)74614-1] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Experimental and computer simulation studies have revealed the presence of a glass-like transition in the internal dynamics of hydrated proteins at approximately 200 K involving an increase of the amplitude of anharmonic dynamics. This increase in flexibility has been correlated with the onset of protein activity. Here, we determine the driving force behind the protein transition by performing molecular dynamics simulations of myoglobin surrounded by a shell of water. A dual heat bath method is used with which, in any given simulation, the protein and solvent are held at different temperatures, and sets of simulations are performed varying the temperature of the components. The results show that the protein transition is driven by a dynamical transition in the hydration water that induces increased fluctuations primarily in side chains in the external regions of the protein. The water transition involves activation of translational diffusion and occurs even in simulations where the protein atoms are held fixed.
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Affiliation(s)
- Alexander L Tournier
- Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, 69120 Heidelberg, Germany
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91
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Paciaroni A, Orecchini A, Cinelli S, Onori G, Lechner R, Pieper J. Protein dynamics on the picosecond timescale as affected by the environment: a quasielastic neutron scattering study. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00102-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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92
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Hayward JA, Daniel RM, Finney JL, Smith JC. Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: a small protein in various environments. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00080-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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93
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Hayward JA, Finney JL, Daniel RM, Smith JC. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophys J 2003; 85:679-85. [PMID: 12885619 PMCID: PMC1303193 DOI: 10.1016/s0006-3495(03)74511-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2002] [Accepted: 02/14/2003] [Indexed: 11/24/2022] Open
Abstract
Molecular dynamics simulations are performed of bovine pancreatic trypsin inhibitor in a cryosolution over a range of temperatures from 80 to 300 K and the origins identified of elastic dynamic neutron scattering from the solution. The elastic scattering and mean-square displacement calculated from the molecular dynamics trajectories are in reasonable agreement with experiments on a larger protein in the same solvent. The solvent and protein contributions to the scattering from the simulation model are determined. At lower temperatures (< approximately 200 K) or on shorter timescales ( approximately 10 ps) the scattering contributions are proportional to the isotopic nuclear scattering cross-sections of each component. However, for T > 200 K marked deviations from these cross-sections are seen due to differences in the dynamics of the components of the solution. Rapid activation of solvent diffusion leads to the variation with temperature of the total elastic intensity being determined largely by that of the solvent. At higher temperatures (>240 K) and longer times ( approximately 100 ps) the protein makes the only significant contribution to the scattering, the solvent scattering having moved out of the accessible time-space window. Decomposition of the protein mean-square displacement shows that the observed dynamical transition in the solution at 200-220 K involves activation of both internal motions and external whole-molecule rotational and translational diffusion. The proportion that the external dynamics contributes to the protein mean-square displacement increases to approximately 30 and 60% at 300 K on the 10- and 100-ps timescales, respectively.
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Affiliation(s)
- Jennifer A Hayward
- Interdisciplinary Centre for Computational Science (JWR), University of Heidelberg, Heidelberg, Germany
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94
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He L, André S, Siebert HC, Helmholz H, Niemeyer B, Gabius HJ. Detection of ligand- and solvent-induced shape alterations of cell-growth-regulatory human lectin galectin-1 in solution by small angle neutron and x-ray scattering. Biophys J 2003; 85:511-24. [PMID: 12829506 PMCID: PMC1303107 DOI: 10.1016/s0006-3495(03)74496-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The bioactivity of galectin-1 in cell growth regulation and adhesion prompted us to answer the questions whether ligand presence and a shift to an aprotic solvent typical for bioaffinity chromatography might alter the shape of the homodimeric human lectin in solution. We used small angle neutron and synchrotron x-ray scattering studies for this purpose. Upon ligand accommodation, the radius of gyration of human galectin-1 decreased from 19.1 +/- 0.1 A in the absence of ligand to 18.2 +/- 0.1 A. In the aprotic solvent dimethyl sulfoxide, which did not impair binding capacity, galectin-1 formed dimers of a dimer, yielding tetramers with a cylindrical shape. Intriguingly, no dissociation into subunits occurred. In parallel, NMR monitoring was performed. The spectral resolution was in accord with these data. In contrast to the properties of the human protein, a nonhomologous agglutinin from mistletoe sharing galactose specificity was subject to a reduction in the radius of gyration from approximately 62 A in water to 48.7 A in dimethyl sulfoxide. Evidently, the solvent caused opposite responses in the two tested galactoside-binding lectins with different folding patterns. We have hereby proven that ligand presence and an aprotic solvent significantly affect the shape of galectin-1 in solution.
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Affiliation(s)
- Lizhong He
- Institute for Coastal Research, Physical and Chemical Analysis, Geesthacht, Germany
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95
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96
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Russo D, Pérez J, Zanotti JM, Desmadril M, Durand D. Dynamic transition associated with the thermal denaturation of a small Beta protein. Biophys J 2002; 83:2792-800. [PMID: 12414711 PMCID: PMC1302363 DOI: 10.1016/s0006-3495(02)75288-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We studied the temperature dependence of the picosecond internal dynamics of an all-beta protein, neocarzinostatin, by incoherent quasielastic neutron scattering. Measurements were made between 20 degrees C and 71 degrees C in heavy water solution. At 20 degrees C, only 33% of the nonexchanged hydrogen atoms show detectable dynamics, a number very close to the fraction of protons involved in the side chains of random coil structures, therefore suggesting a rigid structure in which the only detectable diffusive movements are those involving the side chains of random coil structures. At 61.8 degrees C, although the protein structure is still native, slight dynamic changes are detected that could reflect enhanced backbone and beta-sheet side-chain motions at this higher temperature. Conversely, all internal dynamics parameters (amplitude of diffusive motions, fraction of immobile scatterers, mean-squared vibration amplitude) rapidly change during heat-induced unfolding, indicating a major loss of rigidity of the beta-sandwich structure. The number of protons with diffusive motion increases markedly, whereas the volume occupied by the diffusive motion of protons is reduced. At the half-transition temperature (T = 71 degrees C) most of backbone and beta-sheet side-chain hydrogen atoms are involved in picosecond dynamics.
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Affiliation(s)
- Daniela Russo
- Laboratoire Léon Brillouin, CE Saclay, 91191 Gif-sur-Yvette Cédex, France
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97
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Paciaroni A, Cinelli S, Onori G. Effect of the environment on the protein dynamical transition: a neutron scattering study. Biophys J 2002; 83:1157-64. [PMID: 12124295 PMCID: PMC1302217 DOI: 10.1016/s0006-3495(02)75239-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We performed an elastic neutron scattering investigation of the molecular dynamics of lysozyme solvated in glycerol, at different water contents h (grams of water/grams of lysozyme). The marked non-Gaussian behavior of the elastic intensity was studied in a wide experimental momentum transfer range, as a function of the temperature. The internal dynamics is well described in terms of the double-well jump model. At low temperature, the protein total mean square displacements exhibit an almost linear harmonic trend irrespective of the hydration level, whereas at the temperature T(d) a clear changeover toward an anharmonic regime marks a protein dynamical transition. The decrease of T(d) from approximately 238 K to approximately 195 K as a function of h is reminiscent of that found in the glass transition temperature of aqueous solutions of glycerol, thus suggesting that the protein internal dynamics as a whole is slave to the environment properties. Both T(d) and the total mean square displacements indicate that the protein flexibility strongly rises between 0.1 and 0.2h. This hydration-dependent dynamical activation, which is similar to that of hydrated lysozyme powders, is related to the specific interplay of the protein with the surrounding water and glycerol molecules.
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Affiliation(s)
- Alessandro Paciaroni
- Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica dell'Università di Perugia, Perugia 06121, Italy.
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98
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Bizzarri AR, Cannistraro S. Molecular Dynamics of Water at the Protein−Solvent Interface. J Phys Chem B 2002. [DOI: 10.1021/jp020100m] [Citation(s) in RCA: 440] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Rita Bizzarri
- Unita' INFM, Dipartimento di Scienze Ambientali, Universita’ della Tuscia, I-01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Unita' INFM, Dipartimento di Scienze Ambientali, Universita’ della Tuscia, I-01100 Viterbo, Italy
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99
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Hayward JA, Smith JC. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophys J 2002; 82:1216-25. [PMID: 11867439 PMCID: PMC1301925 DOI: 10.1016/s0006-3495(02)75478-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The temperature dependence of the internal dynamics of an isolated protein, bovine pancreatic trypsin inhibitor, is examined using normal mode analysis and molecular dynamics (MD) simulation. It is found that the protein exhibits marked anharmonic dynamics at temperatures of approximately 100-120 K, as evidenced by departure of the MD-derived average mean square displacement from that of the harmonic model. This activation of anharmonic dynamics is at lower temperatures than previously detected in proteins and is found in the absence of solvent molecules. The simulation data are also used to investigate neutron scattering properties. The effects are determined of instrumental energy resolution and of approximations commonly used to extract mean square displacement data from elastic scattering experiments. Both the presence of a distribution of mean square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean square displacement obtained.
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Affiliation(s)
- Jennifer A Hayward
- Lehrstuhl für Biocomputing, IWR, Universität Heidelberg, D-69120 Heidelberg, Germany
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100
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Librizzi F, Viappiani C, Abbruzzetti S, Cordone L. Residual water modulates the dynamics of the protein and of the external matrix in “trehalose coated ” MbCO: An infrared and flash-photolysis study. J Chem Phys 2002. [DOI: 10.1063/1.1426409] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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